qtl (version 1.70)

mqmprocesspermutation: Convert mqmmulti objects into a scanoneperm object

Description

Function to convert mqmmulti objects into a scanoneperm object, this allows the use of R/qtl methods for permutation analysis that do not support the output of a multiple QTL scan using mqm's outputstructure.

Usage

mqmprocesspermutation(mqmpermutationresult = NULL)

Value

Output of the algorithm is a scanoneperm object. See also: summary.scanoneperm

Arguments

mqmpermutationresult

mqmmulti object obtained after performing permutations on a single trait.using the function mqmpermutation

Author

Ritsert C Jansen; Danny Arends; Pjotr Prins; Karl W Broman

See Also

• The MQM tutorial: https://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

# QTL at chromosome 3
f2qtl <- c(3,15,1,0)

# Mouse genetic map
data(map10)

map10 <- map10[1:3]
# Simulate a F2 Cross
f2cross <- sim.cross(map10,f2qtl,n=100,type="f2")
if (FALSE) # Bootstrap MQM mapping on the f2cross
f2result <- mqmpermutation(f2cross,scanfunction=mqmscan)
f2result <- mqmpermutation(f2cross,scanfunction=mqmscan, n.perm=2, batchsize=2)

# Create a permutation object
f2perm <- mqmprocesspermutation(f2result)

# What LOD score is considered significant?
summary(f2perm)